| b02adab | Thomas B. Mooney | 16 December 2014, 23:01:10 UTC | Merge pull request #327 from tmooney/skip_genotypes_without_references Skip genotype models without references. | 16 December 2014, 23:01:10 UTC |
| 3462e24 | Thomas B. Mooney | 16 December 2014, 20:27:12 UTC | Merge pull request #330 from tmooney/explicitly_create_bridge Create the bridge entities more explicitly. | 16 December 2014, 20:27:12 UTC |
| bb7731f | Adam Coffman | 16 December 2014, 19:57:45 UTC | Merge pull request #322 from acoffman/remove_unused_bx_params_for_sr Remove unused inputs_id and params_id fields in SoftwareResult | 16 December 2014, 19:57:45 UTC |
| 7f3ef7e | Travis Abbott | 16 December 2014, 19:39:35 UTC | Merge pull request #326 from tabbott/aligner-cleanup bwa mem aligner module cleanup | 16 December 2014, 19:39:35 UTC |
| 7909b21 | Feiyu Du | 16 December 2014, 19:21:26 UTC | Merge pull request #321 from dufeiyu/recreate_per_lane_bam Command to recreate per lane bam from a merged bam | 16 December 2014, 19:21:26 UTC |
| 01fb1b5 | Thomas Mooney | 16 December 2014, 18:50:22 UTC | Create the bridge entities more explicitly. UR tries to find an "add_analysis_project" subroutine, which does not exist. So call something that does exist instead. | 16 December 2014, 18:50:22 UTC |
| 0704b3c | Feiyu Du | 16 December 2014, 18:06:35 UTC | change parameter names and use transient variable _output_dir | 16 December 2014, 18:06:35 UTC |
| 6273389 | Thomas B. Mooney | 16 December 2014, 18:05:15 UTC | Merge pull request #261 from tmooney/fl_merge_refseq_handling Improved Feature-List Merge Support | 16 December 2014, 18:05:15 UTC |
| facb705 | Jim Weible | 16 December 2014, 18:02:51 UTC | Merge pull request #329 from jweible/br_locking_fix fix build_requested locking so that it only locks if we modify the value | 16 December 2014, 18:02:51 UTC |
| 829f97f | Jim Weible | 16 December 2014, 16:49:57 UTC | fix build_requested locking so that it only locks if we modify the value, because derp | 16 December 2014, 16:49:57 UTC |
| b1762e2 | Thomas Mooney | 16 December 2014, 16:15:22 UTC | Skip genotype models without references. The reference can't match our reference if it doesn't exist! | 16 December 2014, 16:15:22 UTC |
| b5553a0 | Thomas B. Mooney | 16 December 2014, 15:32:29 UTC | Merge pull request #295 from tmooney/config_deduplicate_errors Some Deduplication of Status Checking | 16 December 2014, 15:32:29 UTC |
| 0ade44b | Susanna Siebert | 16 December 2014, 15:16:19 UTC | Merge pull request #323 from susannasiebert/fireteam Fix misspelled parameter usage | 16 December 2014, 15:16:19 UTC |
| c83c8d3 | APipe Tester | 16 December 2014, 13:18:41 UTC | Updated `gmt` tab completion. | 16 December 2014, 13:18:41 UTC |
| 2ab047d | APipe Tester | 16 December 2014, 13:17:52 UTC | Updated `genome` tab completion. | 16 December 2014, 13:17:52 UTC |
| 2ba2657 | APipe Tester | 16 December 2014, 13:14:18 UTC | Updated class browser cache. | 16 December 2014, 13:14:18 UTC |
| ec0a00f | Travis Abbott | 16 December 2014, 03:35:29 UTC | more cleanup of paths that were using str concat everywhere | 16 December 2014, 03:35:29 UTC |
| f469200 | Travis Abbott | 16 December 2014, 02:50:41 UTC | add methods for finding faidx / bwa indexed fastas | 16 December 2014, 02:50:41 UTC |
| aa51cbb | Gabriel Sanderson | 16 December 2014, 01:54:00 UTC | Merge pull request #320 from apregier/tcga_fixes Tcga fixes | 16 December 2014, 01:54:00 UTC |
| bd7ec9c | Travis Abbott | 16 December 2014, 01:32:08 UTC | add more tests for bwa mem aligner module I need a test that actually aligns something. | 16 December 2014, 01:32:08 UTC |
| f260d0b | Travis Abbott | 15 December 2014, 22:03:36 UTC | add some tests for bwamem alignment module | 16 December 2014, 00:03:33 UTC |
| 5ca5963 | Feiyu Du | 15 December 2014, 22:32:44 UTC | Make changes based on PR code review | 15 December 2014, 22:32:44 UTC |
| b5463f8 | Susanna Siebert | 15 December 2014, 22:08:03 UTC | Also fix the corresponding error message | 15 December 2014, 22:08:03 UTC |
| dc8e659 | Travis Abbott | 13 December 2014, 02:40:10 UTC | trailing whitespace DO NOT WANT | 15 December 2014, 21:46:30 UTC |
| f9310b2 | Travis Abbott | 13 December 2014, 02:36:09 UTC | refactor sam header creation in alignment result I'm planning to make some changes that want access to the read group information in the generated sam header, so I pulled the relevant code out into a function and added some more specific tests about sam header generation. | 15 December 2014, 21:46:30 UTC |
| 766116b | Ian Ferguson | 11 December 2014, 21:49:48 UTC | Remove references to {input,param}_{id,bx} | 15 December 2014, 21:45:06 UTC |
| bbbdbea | Adam Coffman | 11 December 2014, 21:27:15 UTC | remove un-used {input,param}_{id,bx} properties | 15 December 2014, 21:44:45 UTC |
| 301502f | Travis Abbott | 10 December 2014, 22:38:11 UTC | remove unused test class for intermediate alignment results | 15 December 2014, 21:43:36 UTC |
| 2aa863a | Susanna Siebert | 15 December 2014, 21:41:52 UTC | fix misspelled parameter usage | 15 December 2014, 21:41:52 UTC |
| f0c9d47 | Travis Abbott | 15 December 2014, 21:39:15 UTC | Merge pull request #313 from tabbott/bwa-mem-tmp add gmt bwa run-mem | 15 December 2014, 21:39:15 UTC |
| 4d87991 | Travis Abbott | 15 December 2014, 21:07:54 UTC | use File::Spec->catfile instead of sprintf to form paths meow | 15 December 2014, 21:07:54 UTC |
| 2b454d8 | Travis Abbott | 15 December 2014, 21:01:35 UTC | update errors to use die $self->error_message | 15 December 2014, 21:01:35 UTC |
| 88b0ac0 | Travis Abbott | 15 December 2014, 20:57:57 UTC | fix adding of thread params to bwa cmdline oops, forgot () around list | 15 December 2014, 20:57:57 UTC |
| 45a11f4 | Travis Abbott | 15 December 2014, 20:57:34 UTC | more detailed error reporting for failure cases | 15 December 2014, 20:57:34 UTC |
| 2d307e5 | Travis Abbott | 15 December 2014, 20:52:33 UTC | remove redundant definition of pipeline commands | 15 December 2014, 20:52:33 UTC |
| 8338d41 | Thomas Mooney | 15 December 2014, 19:32:52 UTC | Add a test that compares the error we got with the error we expected. | 15 December 2014, 19:32:52 UTC |
| 215a865 | Adam Coffman | 15 December 2014, 19:20:17 UTC | Merge pull request #265 from acoffman/stop_creating_anp_model_groups Stop creating AnP ModelGroups | 15 December 2014, 19:20:17 UTC |
| 3a154af | Adam Coffman | 15 December 2014, 18:53:47 UTC | Merge pull request #316 from acoffman/factor_out_timings_in_sr Factor timing implementation out of SoftwareResult | 15 December 2014, 18:53:47 UTC |
| 18a8e83 | Feiyu Du | 15 December 2014, 18:50:45 UTC | make samtools/picard version not optional | 15 December 2014, 18:50:45 UTC |
| e8a349e | Jim Weible | 15 December 2014, 18:33:49 UTC | Merge pull request #286 from jweible/AUE-382 Locking around build_requested for race condition (AUE-382) | 15 December 2014, 18:33:49 UTC |
| cc8252c | APipe Tester | 15 December 2014, 17:13:37 UTC | updated graphite submodule to 8a08a11 | 15 December 2014, 18:20:25 UTC |
| 199affc | APipe Tester | 15 December 2014, 17:13:26 UTC | updated jenkins submodule to 787c4e4 | 15 December 2014, 18:20:24 UTC |
| 8a252cd | APipe Tester | 15 December 2014, 17:13:07 UTC | updated ur submodule to a39cdc3 | 15 December 2014, 18:20:24 UTC |
| 94dafc2 | Indraniel | 15 December 2014, 18:07:47 UTC | Merge pull request #301 from indraniel/BIO-1229-clean-fastqs + clean up FASTQs in /tmp after bwamem finishes aligning | 15 December 2014, 18:07:47 UTC |
| c3282a7 | David Morton | 15 December 2014, 17:54:39 UTC | Merge pull request #317 from davidlmorton/library_vaf Fix vaf calculations | 15 December 2014, 17:54:39 UTC |
| 90c3575 | Thomas B. Mooney | 15 December 2014, 16:59:50 UTC | Merge pull request #308 from tmooney/sr_is_id_query Fix SR's `_is_id_only_query` | 15 December 2014, 16:59:50 UTC |
| 21c33ff | apregier | 15 December 2014, 16:48:39 UTC | Don't set target file info for imported builds | 15 December 2014, 16:48:39 UTC |
| ea29cc1 | apregier | 15 December 2014, 16:47:35 UTC | Move method Other classes also need to ask the build if it has imported instrument data | 15 December 2014, 16:47:35 UTC |
| 4a1e322 | apregier | 15 December 2014, 16:39:52 UTC | TCGA archive creator matches main IDF spec | 15 December 2014, 16:39:52 UTC |
| 77aa8b6 | Jim Weible | 15 December 2014, 16:23:09 UTC | File::Spec it up | 15 December 2014, 16:23:09 UTC |
| 38254e5 | Thomas Mooney | 15 December 2014, 16:14:34 UTC | Test that __errors__ is checking our statuses. | 15 December 2014, 16:14:34 UTC |
| 9498129 | Thomas Mooney | 15 December 2014, 15:59:38 UTC | Test that we're manipulating subclass documentation. | 15 December 2014, 16:02:18 UTC |
| 4f33e0c | Thomas Mooney | 15 December 2014, 15:45:38 UTC | Convert valid_statuses to an ordinary subroutine. | 15 December 2014, 16:02:18 UTC |
| 63351f6 | Jim Weible | 15 December 2014, 14:52:53 UTC | Lock to the process context and unlock only once | 15 December 2014, 14:52:53 UTC |
| 0212b3d | Jim Weible | 15 December 2014, 14:52:08 UTC | use more intelligent lock params | 15 December 2014, 14:52:08 UTC |
| 73a2b3a | David Morton | 13 December 2014, 04:47:15 UTC | Merge pull request #304 from davidlmorton/genome-test-inputs-transition This removes /gscmnt/gc13003 from test data | 13 December 2014, 04:47:15 UTC |
| 8f7cc8d | Travis Abbott | 13 December 2014, 02:18:15 UTC | perl => genome-perl as interpreter in test do want. | 13 December 2014, 02:18:15 UTC |
| 84b1b7e | Travis Abbott | 13 December 2014, 00:45:45 UTC | add samtools_version param a little weird, as this module insists on 0.1.19 (trying to use another version will earn you an exception), but maybe nice for documentation purposes. | 13 December 2014, 00:45:45 UTC |
| a7485e8 | Travis Abbott | 13 December 2014, 00:43:06 UTC | die when aligner_params contains -t we used to silently remove any threading options from the aligner params. now, we get offended at the lack of respect for the --num-threads parameter and throw and exception. | 13 December 2014, 00:43:06 UTC |
| d56fcf6 | Nathaniel Nutter | 12 December 2014, 23:30:24 UTC | Merge pull request #318 from nnutter/symlink update symlink so it used current GENOME_TEST_INPUTS | 12 December 2014, 23:30:24 UTC |
| 6bb3c52 | Nathaniel Nutter | 12 December 2014, 22:56:08 UTC | update symlink so it used current GENOME_TEST_INPUTS | 12 December 2014, 22:56:08 UTC |
| e2b1c8d | dmorton | 12 December 2014, 19:10:48 UTC | Fix vaf calculations For per-library vaf: Instead of dividing by the total depth (across all libraries) we need to divide by the depth in just that one library. For total vaf: Instead of summing up per-library vaf we need to calculate the coverage and depth directly. | 12 December 2014, 20:14:14 UTC |
| 3d0f081 | Adam Coffman | 12 December 2014, 20:00:37 UTC | remove trailing whitespace | 12 December 2014, 20:00:37 UTC |
| a97111f | Adam Coffman | 12 December 2014, 19:49:22 UTC | factor timing code out of _faster_get | 12 December 2014, 19:49:22 UTC |
| b41eb3c | Adam Coffman | 12 December 2014, 19:26:05 UTC | Merge pull request #312 from acoffman/allow_multiple_metrics_in_timing Allow multiple metrics with the same timing code. | 12 December 2014, 19:26:05 UTC |
| 32184bc | Feiyu Du | 12 December 2014, 18:14:15 UTC | temporarily change the path of seq-grind0.1 to pass the test | 12 December 2014, 18:14:15 UTC |
| b8087a7 | Adam Coffman | 11 December 2014, 22:43:09 UTC | allow multiple metrics for the same timing code | 12 December 2014, 18:12:26 UTC |
| 05937f2 | Indraniel Das | 12 December 2014, 17:51:03 UTC | + refactor for loop in show_temporary_input_files_queue - this is @brummett's second suggestion in github's genome pull request 301 https://github.com/genome/genome/pull/301 | 12 December 2014, 17:51:03 UTC |
| d7e0991 | Indraniel Das | 12 December 2014, 17:50:34 UTC | + remove needless pass statement in test | 12 December 2014, 17:50:34 UTC |
| 2f4e178 | Indraniel Das | 12 December 2014, 17:44:32 UTC | + make an explicit debug message when the temp queue is empty | 12 December 2014, 17:44:32 UTC |
| e76fda1 | Indraniel Das | 12 December 2014, 17:40:01 UTC | + make the add items to the temporary queue public - this is @brummett's first suggestion in github's genome pull request 301. https://github.com/genome/genome/pull/301 | 12 December 2014, 17:40:01 UTC |
| f9251cf | apregier | 12 December 2014, 16:45:05 UTC | Merge pull request #315 from apregier/fix_model_report_indel_plan Fix bug with somatic indels plan file | 12 December 2014, 16:45:05 UTC |
| 73030e1 | Susanna Siebert | 12 December 2014, 16:34:51 UTC | Merge pull request #310 from susannasiebert/epitope_prediction Use alternate snvs file if snvs.hq.tier1.v1.annotated.top.header doesn't exist | 12 December 2014, 16:34:51 UTC |
| 2aa1cf2 | apregier | 12 December 2014, 16:30:23 UTC | Fix bug with somatic indels plan file | 12 December 2014, 16:31:12 UTC |
| 1a023fe | APipe Tester | 12 December 2014, 13:16:38 UTC | Updated `gmt` tab completion. | 12 December 2014, 13:16:38 UTC |
| e4aed1a | APipe Tester | 12 December 2014, 13:15:55 UTC | Updated `genome` tab completion. | 12 December 2014, 13:15:55 UTC |
| 1c3db49 | Travis Abbott | 12 December 2014, 04:54:59 UTC | update to look at $PIPEFAIL in bash | 12 December 2014, 04:54:59 UTC |
| a097853 | Travis Abbott | 12 December 2014, 03:07:43 UTC | fix typo in help | 12 December 2014, 03:07:43 UTC |
| e5f40ea | Travis Abbott | 12 December 2014, 02:24:19 UTC | add gmt bwa run-mem A command to map fastqs to coordinate sorted bam files with bwa mem. | 12 December 2014, 02:24:19 UTC |
| 71a37b2 | David Morton | 11 December 2014, 23:47:58 UTC | Merge pull request #311 from susannasiebert/variant_reporting_igv Bed report needs to write .bed file for igv xml to work | 11 December 2014, 23:47:58 UTC |
| 842280f | Feiyu Du | 11 December 2014, 22:39:21 UTC | Add command tool to receate per lane bam | 11 December 2014, 22:39:21 UTC |
| 654a422 | Gabriel Sanderson | 11 December 2014, 22:11:28 UTC | Merge pull request #296 from gsanders/tcga_bgzip CreateSubmissionArchive bgzips vcfs before generating manifest | 11 December 2014, 22:11:28 UTC |
| 9af6494 | Susanna Siebert | 11 December 2014, 21:26:24 UTC | bed reporter needs to write .bed file for igv xml to work | 11 December 2014, 21:26:24 UTC |
| ecb2db6 | Travis Abbott | 11 December 2014, 20:04:04 UTC | Merge pull request #309 from tabbott/sv-fileformats Sv fileformats | 11 December 2014, 20:04:04 UTC |
| 33e563a | Indraniel Das | 11 December 2014, 17:45:59 UTC | + place temp fastq files in queue closer to their creation - this is @tmooney's recommend idea. See commentary at: https://github.com/indraniel/genome/commit/dddbd5920c8ccd49b2a261395807f71631097957 | 11 December 2014, 17:45:59 UTC |
| 2d10830 | Indraniel Das | 11 December 2014, 17:44:18 UTC | + initial the default temp_input_files queue array in class definition - this is more idiomatic in Genome | 11 December 2014, 17:44:18 UTC |
| 47e0591 | Susanna Siebert | 11 December 2014, 13:49:33 UTC | Use the snvs.hq.tier1.v1.annotated.top file if snvs.hq.tier1.v1.annotated.top.header doesn't exist | 11 December 2014, 13:49:39 UTC |
| ea5b8f2 | Travis Abbott | 11 December 2014, 01:15:26 UTC | update G/F/Breakdancer to be able to parse Squaredancer files Squaredancer reports SVs in Breakdancer format with one notable exception: the orientation fields. Breakdancer always reports + and - counts (even when one is zero): 10+0- Squaredancer can report for only one strand, like so: 10+ The parsing code now handles both possibilities. | 11 December 2014, 01:15:26 UTC |
| 84cdf5a | Travis Abbott | 11 December 2014, 01:12:58 UTC | add "make_header_line" function to G/F/Bedpe/Header When called on an empty header, the proper header line will be generated and added (including the standard and any custom fields). When called on a non-empty header, an exception is thrown. | 11 December 2014, 01:12:58 UTC |
| 7b14f98 | Indraniel Das | 10 December 2014, 23:31:35 UTC | + remove DB::single in AlignmentResult.t test - oops! | 10 December 2014, 23:31:35 UTC |
| 7388cb3 | Thomas Mooney | 10 December 2014, 23:16:42 UTC | Always define the boolean expression. | 10 December 2014, 23:16:42 UTC |
| dddbd59 | Indraniel Das | 10 December 2014, 23:14:29 UTC | + clean up FASTQs in /tmp -- take two - this is a second refactor attempt after a discussion in [github genome pull request 301][1] and further offline discussion with @tabbott. - this is midway refactor. @tabbott's original lambda suggestion is probably the best way to do things long-term, but the desired refactor may get unwieldy and out of scope for immediate needs. The basic goal is to place the temporary file deletion logic in the base class, rather than in the subclass. This is because the input files supplied to the aligners get generated in the base class. - The Bwamem test: lib/perl/Genome/InstrumentData/AlignmentResult/Bwamem.t as been reset back to the original version before this feature branch started. [1]: https://github.com/genome/genome/pull/301/ | 10 December 2014, 23:14:29 UTC |
| 76e92c9 | Thomas B. Mooney | 10 December 2014, 23:11:40 UTC | Merge pull request #302 from tmooney/update_mg_copy_for_ur_update Use regex directly in Genome::ModelGroup::Command::Copy. | 10 December 2014, 23:11:40 UTC |
| 93b60f3 | Thomas Mooney | 10 December 2014, 22:19:07 UTC | Revert "Avoid using SR->get with args other than ID" This reverts commit 01258c6d5376e4e0645654942419cfda908951e4. It should no longer be necessary with the SR fix. | 10 December 2014, 22:44:38 UTC |
| 19e2f2b | Thomas Mooney | 10 December 2014, 22:42:33 UTC | Fix case of Genome::SoftwareResult->get(id => 'xxxx') | 10 December 2014, 22:42:33 UTC |
| bd94a0c | apregier | 10 December 2014, 22:13:03 UTC | Merge pull request #303 from davidlmorton/avoid-sr-get Avoid using SR->get with args other than ID | 10 December 2014, 22:13:03 UTC |
| b3b296b | apregier | 10 December 2014, 22:08:36 UTC | Merge pull request #305 from apregier/fix_coverage_summary_for_cle Fix coverage summary for cle | 10 December 2014, 22:08:36 UTC |
| ca03b7e | apregier | 10 December 2014, 22:08:14 UTC | Merge pull request #307 from apregier/fix_library_names_for_cle_full_report Fix library names for cle full report | 10 December 2014, 22:08:14 UTC |
| 0571700 | Gabriel Sanderson | 10 December 2014, 21:50:12 UTC | The sdrf file now contains the compressed vcf name if appropriate | 10 December 2014, 21:50:12 UTC |
| 1253f2c | apregier | 10 December 2014, 21:28:38 UTC | Somatic validation builds need to get the region_of_interest_set_name indirectly | 10 December 2014, 21:34:17 UTC |
